Research Software

The computational tools I develop in my own work are often useful beyond that particular question. I aim to generalize these solutions for the use in other fields, and package them as open research software. You can follow my software development activity on github.

Software packages I am a lead developer for

moultmcmc
This R package provides Bayesian inference for models of avian primary moult.

deBInfer: Bayesian inference for dynamical models of biological systems in R (with SJ Ryan and LR Johnson)
An R framework for Bayesian parameter inference in ordinary and delay differential equation models.

rucrdtw
Fast time series subsequence search under dynamic time warping in R. This package provides R bindings for functions from the UCR Suite.

ewp: Exponentially weighted Poisson regression
Modelling interface for underdispersed count data.

seabirdeb
This R package provides compiled dynamic energy budget models for seabirds.

DEButilities
This R package provides functions to facilitate dynamic energy budget model parameter estimation with deBInfer.

microclimloggers
This package provides functions to parse and reshape microclimate logger data (e.g. iButton Hygrochron, HOBO pendant loggers).

Other contributions

Software is fundamental to modern ecological research, yet it is poorly integrated in todays scholarly practice, and receives little acknowledgement in the scholarly record. I strongly believe that research software should be treated on the same basis as other scholarly products such as papers, books, and data sets. Research software deserves peer-review and citations.

I strive to support reproducible research and sustainable research software development as a Fellow of the Software Sustainability Institute, member of the Carpentries community, and as a reviewer and contributor to journals like JORS, JOSS, and ReScience. Many of my contributions are public on github.